Supporters of the ousted president have called the election illegitimate and ahead of the vote Zelaya called for a boycott.
Speaking to Al Jazeera on Monday, Zelaya said he had evidence that Hondurans had refused to turn out for the election and that the vote had "no respect and no credibility".
"We took a sample at the polls and the rate of abstentions was over 60 per cent in most cases," he said.
"This means the election had low turnout, which means it did not enjoy the support of the majority of the Honduran people."
Zelaya was speaking from inside the Brazilian mission in Tegucigalpa, the Honduran capital, where he has taken refuge since returning to the country several weeks ago.
"We are fighting a dictatorship and until we defeat it we will not be satisfied," Zelaya told Al Jazeera.
Tomas Andino, an activist for a group called the National Resistance Front, which is against Micheletti's administration, also said that turnout had been low.
"Anyone who has wandered about the city of Tegucigalpa or other cities of Honduras will realise that the number of people who went to the polls was really minimal," he told Al Jazeera.
Craig Mauro, Al Jazeera's reporter in Tegucigalpa, said turnout had been very low in the city's poorer districts where support for Zelaya is strongest, but had been much higher in wealthier areas.
Officials insisted voter turnout was over 60 per cent.
Neither Zelaya nor the man who replaced him - Roberto Micheletti, the de facto president – ran in the vote and the election has been largely shunned by international monitors.
Many regional powers, including the United States, have been divided over whether or not to recognise the outcome of the election.
Hondurans vote amid calls to boycott polls aimed at ending political crisis
Analysts say how much credibility the vote will be given will depend to a large extent on voter turnout.
Some Latin American countries such as Brazil, Venezuela and Argentina have already said they will not back the result.
Luiz Inacio Lula da Silva, Brazil's president, told reporters: "It's not possible to accept a coup, whether it's a military coup or dressed up as a civilian coup."
But the US has said that as long as the poll is shown to be free and fair, an election is the only way to resolve Honduras' political standoff.
Lobo and Santos, both prosperous businessmen, have been clear front-runners in the vote, though their campaigns have been overshadowed by the debate over the vote's legitimacy.
Lobo has said that if he wins, he will plead with foreign leaders to restore funding and seek a new agreement with the International Monetary Fund.
Honduras has been shut out by foreign donors since the June 28 coup, badly damaging the economy of one of Latin America's poorest nations.
Tensions were high across the country as voting got under way on Sunday, and in the northern city of San Pedro clashes broke out after police fired tear gas at several hundred pro-Zelaya protesters.
At least one person was injured and several of the protesters hurled rocks back at police.
|Many supporters of Zelaya were expected to support his call for a boycott [Reuters]
However there were no reports of major unrest elsewhere in the country and reports said voting day had passed off calmly in Tegucigalpa.
The election was organised before Zelaya was removed from power, with the candidates chosen in primaries last year.
"These elections would have been the same, whether Zelaya had been there or not," Edward Schumacher-Matos, a newspaper columnist and Latin America analyst, said.
"You had a constitutional crisis that was precipitated by the president himself," he told Al Jazeera in New York.
"He was ordered arrested by the supreme court for violating the constitution. He tried to carry out a referendum that the supreme court, the congress, his own attorney-general and the human rights ombudsman all said was a violation of the constitution and illegal."
Zelaya had called for a vote asking the public whether they would support attempts to remove the one-term limit for the presidency set out in the constitution.